# HG changeset patch
# User dcorreia
# Date 1485175376 18000
# Node ID 814b453382cf23882a1446602b2690774ca7a543
# Parent 029e38c5063a6874ffd6db76f0ddd80f2e637dd5
Uploaded
diff -r 029e38c5063a -r 814b453382cf test-data/nad3.pir
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nad3.pir Mon Jan 23 07:42:56 2017 -0500
@@ -0,0 +1,101 @@
+>P1;nad3_parde
+
+------MEYLLQEYLPILVFLGMASALAIVLILAAAVIAVRN--PDPEKVSAYECGFNAF
+D-DARMKFDVRFYLVSILFIIFDLEVAFLFPWAVSFASLS-DVAFWGLMVFLAVLTVGFA
+YEWKKGALEWA----------------------*
+
+>P1;nad3_acaca
+
+---------MTLEYIYIFIFFWGAFFISCLLIFLSYFLVYQE--SDIEKNSAYECGFQPF
+E-DTRSKFNVRYYLIAILFMIFDLEIMYLFPWSISISTGS-FFGVWAIFLFLIILTVGFI
+YEWQKGALEWD----------------------*
+
+>P1;nad3_allma
+
+--------------MTYLVYIVFTIVLTVGLILVSYLLSQAQ--PDSEKVSAYECGFSPL
+G-DARQKFDVSFYLIAILFIIFDLEVVFILPFASVIHNVS-LLGGWITIIFLVILTIGFI
+YEFVSGAITDSF---------------------*
+
+>P1;nad3_apec
+
+-----------IFNFLTLFVSILIFLITTLITFAAHFLPSRN-TD-SEKSSPYECGFDPL
+N-SARVPFSFRFFLVAILFLLFDLEIALLFPLPFSVFFH--P--IHTP----LILTVGLI
+FEWVQGGLDWAE---------------------*
+
+>P1;nad3_arath
+
+---------MMSEFAPISIYLVISLLVSLILLGVPFPFASNS-STYPEKLSAYECGFDPS
+G-DARSRFDIRFYLVSILFLIPDLEVTFFFPWAVPPNKID-LFGFWSMMAFLFILTIGFL
+YEWKRGASDRE----------------------*
+
+>P1;nad3_balca
+
+-------------MNSFLIYLLIAITLSFILSIVGHRLPTRN-MD-QEKLSPYECGFDPQ
+A-SARLPFSLRFFLVAILFLLFDLEIALLLPFPAALSARDPQLSFTLAFLILLILTIGLI
+YEWMEGGLEWAE---------------------*
+
+>P1;nad3_chocr
+
+------MKLIFTEYSAILIFFAISSLLSSVIFLLSYFLIPQK--PDQEKVSAYECGFNPF
+D-DARATFDIRFYLVAILFLIFDLEISFLFPWSLVLGEIS-IIGFWSMIVFLVILTIGFI
+YEWYKGALEWE----------------------*
+
+>P1;nad3_drome
+
+-------------MFSIIFIALLILLITTIVMFLASILSKKA-LIDREKSSPFECGFDPK
+S-SSRLPFSLRFFLITIIFLIFDVEIALILPMIIIMKYSNIMIWTITSIIFILILLIGLY
+HEWNQGMLNWSN---------------------*
+
+>P1;nad3_human
+
+-------------MN-FALILMINTLLALLLMIITFWLPQLN-GY-MEKSTPYECGFDPM
+S-PARVPFSMKFFLVAITFLLFDLEIALLLPLPWALQTTNLPLMVMSSLLLIIILALSLA
+YEWLQKGLDWTE---------------------*
+
+>P1;nad3_ktun
+
+-------------MFFVLSLVLFTFLLSLVLLSVSLSLTKKK-MMNREKSSPFECGFDPK
+S-SARLPFSMRFFLITVVFLVFDVEIVLLLPYLFSSGWSIDVFSLVGSMMILVILIIGVL
+HEWSEGSLEWFSSSN------------------*
+
+>P1;nad3_lter
+
+-------------MILTALSSAIALLVPIIILGAAWVLASRS-TEDREKSSPFECGFDPK
+S-TARIPFSTRFFLLAIIFIVFDIEIVLLMPLPTILHTSDVFTTVTTSVLFLMILLIGLI
+HEWKEGSLDWSS---------------------*
+
+>P1;nad3_marpo
+
+-----------MEFAPIFVYLVISLLLSLILIGVSFLFASSSSLAYPEKLSAYECGFDPF
+D-DARSRFDIRFYLVSILFIIFDLEVTFLFPWAVSLNKIG-LFGFWSMMVFLFILTIGFV
+YEWKKGALDWE----------------------*
+
+>P1;nad3_metse
+
+---------MYTEFYGILVLLIFSVVLSAIISGASYILGDKQ--PDREKVSAYECGFDPF
+G-TPGRPFSIRFFLIGILFLIFDLEISFLFPWCVVCNQVF-PFGYWTMIVFLAVLTLGLV
+YEWLKGGLEWE----------------------*
+
+>P1;nad3_picca
+
+MLNYFVYPYGIENDMGMKFYMMLVPMMSMVLMMINYMMTNKS-DNNMNKTGPYECGFDSF
+R-QSRTTYSIKFILIAILFLPFDLELTSILPYTLSMYNTN-IYGLFILLYFLLPLIIGFI
+IEINTKAIYMTKMFNRNVKSMTSYVKYNNKI--*
+
+>P1;nad3_podan
+
+-------------MSSMTLFILFVSIIALLFLFINLIFAPHN--PYQEKYSIFECGFHSF
+LGQNRTQFGVKFFIFALVYLLLDLEILLTFPFAVSEYVNN-IYGLIILLGFITIITIGFV
+YELGKSALKIDSRQVITMTRFNYSSTIEYLGKI*
+
+>P1;nad3_prowi
+
+----------MYEFLGILIYFFIALALSLLLLGLPFLVSTRK--ADPEKISAYECGFDPF
+D-DARGRFDIQFYLVAILFIIFDLEVAFLFPWALTLNKIG-YFGFWSMMLFLFILTVGFI
+YEWRKGALDWS----------------------*
+
+>P1;nad3_recam
+
+-----MNTMILSEYLSVLIFFIFSFGLSCIILGLSYVLATQN--ADTEKLSPYECGFNPF
+D-DARGAFDVRFYLVAILFIIFDLEVAFLFPWAVALSDVT-IFGFWTMFIFLLILTVGFI
+YEWKKGALDWE----------------------*
diff -r 029e38c5063a -r 814b453382cf test-data/nad3.pir-gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nad3.pir-gb Mon Jan 23 07:42:56 2017 -0500
@@ -0,0 +1,68 @@
+>P1;nad3_parde
+
+EKVSAYECGF NAFARMKFDV RFYLVSILFI IFDLEVAFLF PVLTVGFAYE WKKGAL*
+
+>P1;nad3_acaca
+
+EKNSAYECGF QPFTRSKFNV RYYLIAILFM IFDLEIMYLF PILTVGFIYE WQKGAL*
+
+>P1;nad3_allma
+
+EKVSAYECGF SPLARQKFDV SFYLIAILFI IFDLEVVFIL PILTIGFIYE FVSGAI*
+
+>P1;nad3_apec
+
+EKSSPYECGF DPLARVPFSF RFFLVAILFL LFDLEIALLF PILTVGLIFE WVQGGL*
+
+>P1;nad3_arath
+
+EKLSAYECGF DPSARSRFDI RFYLVSILFL IPDLEVTFFF PILTIGFLYE WKRGAS*
+
+>P1;nad3_balca
+
+EKLSPYECGF DPQARLPFSL RFFLVAILFL LFDLEIALLL PILTIGLIYE WMEGGL*
+
+>P1;nad3_chocr
+
+EKVSAYECGF NPFARATFDI RFYLVAILFL IFDLEISFLF PILTIGFIYE WYKGAL*
+
+>P1;nad3_drome
+
+EKSSPFECGF DPKSRLPFSL RFFLITIIFL IFDVEIALIL PILLIGLYHE WNQGML*
+
+>P1;nad3_human
+
+EKSTPYECGF DPMARVPFSM KFFLVAITFL LFDLEIALLL PILALSLAYE WLQKGL*
+
+>P1;nad3_ktun
+
+EKSSPFECGF DPKARLPFSM RFFLITVVFL VFDVEIVLLL PILIIGVLHE WSEGSL*
+
+>P1;nad3_lter
+
+EKSSPFECGF DPKARIPFST RFFLLAIIFI VFDIEIVLLM PILLIGLIHE WKEGSL*
+
+>P1;nad3_marpo
+
+EKLSAYECGF DPFARSRFDI RFYLVSILFI IFDLEVTFLF PILTIGFVYE WKKGAL*
+
+>P1;nad3_metse
+
+EKVSAYECGF DPFPGRPFSI RFFLIGILFL IFDLEISFLF PVLTLGLVYE WLKGGL*
+
+>P1;nad3_picca
+
+NKTGPYECGF DSFSRTTYSI KFILIAILFL PFDLELTSIL PPLIIGFIIE INTKAI*
+
+>P1;nad3_podan
+
+EKYSIFECGF HSFNRTQFGV KFFIFALVYL LLDLEILLTF PIITIGFVYE LGKSAL*
+
+>P1;nad3_prowi
+
+EKISAYECGF DPFARGRFDI QFYLVAILFI IFDLEVAFLF PILTVGFIYE WRKGAL*
+
+>P1;nad3_recam
+
+EKLSPYECGF NPFARGAFDV RFYLVAILFI IFDLEVAFLF PILTVGFIYE WKKGAL*
+
diff -r 029e38c5063a -r 814b453382cf test-data/nad3.pir-gb.htm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nad3.pir-gb.htm Mon Jan 23 07:42:56 2017 -0500
@@ -0,0 +1,124 @@
+
+
+
+nad3.pir
+
+
+
+
+Gblocks 0.91b Results
+
+Processed file: nad3.pir
+Number of sequences: 17
Alignment assumed to be: Protein
+New number of positions: 56 (selected positions are underlined in blue)
+
+
+ 10 20 30 40 50 60
+ =========+=========+=========+=========+=========+=========+
+nad3_parde ------MEYLLQEYLPILVFLGMASALAIVLILAAAVIAVRN--PDPEKVSAYECGFNAF
+nad3_acaca ---------MTLEYIYIFIFFWGAFFISCLLIFLSYFLVYQE--SDIEKNSAYECGFQPF
+nad3_allma --------------MTYLVYIVFTIVLTVGLILVSYLLSQAQ--PDSEKVSAYECGFSPL
+nad3_apec -----------IFNFLTLFVSILIFLITTLITFAAHFLPSRN-TD-SEKSSPYECGFDPL
+nad3_arath ---------MMSEFAPISIYLVISLLVSLILLGVPFPFASNS-STYPEKLSAYECGFDPS
+nad3_balca -------------MNSFLIYLLIAITLSFILSIVGHRLPTRN-MD-QEKLSPYECGFDPQ
+nad3_chocr ------MKLIFTEYSAILIFFAISSLLSSVIFLLSYFLIPQK--PDQEKVSAYECGFNPF
+nad3_drome -------------MFSIIFIALLILLITTIVMFLASILSKKA-LIDREKSSPFECGFDPK
+nad3_human -------------MN-FALILMINTLLALLLMIITFWLPQLN-GY-MEKSTPYECGFDPM
+nad3_ktun -------------MFFVLSLVLFTFLLSLVLLSVSLSLTKKK-MMNREKSSPFECGFDPK
+nad3_lter -------------MILTALSSAIALLVPIIILGAAWVLASRS-TEDREKSSPFECGFDPK
+nad3_marpo -----------MEFAPIFVYLVISLLLSLILIGVSFLFASSSSLAYPEKLSAYECGFDPF
+nad3_metse ---------MYTEFYGILVLLIFSVVLSAIISGASYILGDKQ--PDREKVSAYECGFDPF
+nad3_picca MLNYFVYPYGIENDMGMKFYMMLVPMMSMVLMMINYMMTNKS-DNNMNKTGPYECGFDSF
+nad3_podan -------------MSSMTLFILFVSIIALLFLFINLIFAPHN--PYQEKYSIFECGFHSF
+nad3_prowi ----------MYEFLGILIYFFIALALSLLLLGLPFLVSTRK--ADPEKISAYECGFDPF
+nad3_recam -----MNTMILSEYLSVLIFFIFSFGLSCIILGLSYVLATQN--ADTEKLSPYECGFNPF
+ #############
+
+
+ 70 80 90 100 110 120
+ =========+=========+=========+=========+=========+=========+
+nad3_parde D-DARMKFDVRFYLVSILFIIFDLEVAFLFPWAVSFASLS-DVAFWGLMVFLAVLTVGFA
+nad3_acaca E-DTRSKFNVRYYLIAILFMIFDLEIMYLFPWSISISTGS-FFGVWAIFLFLIILTVGFI
+nad3_allma G-DARQKFDVSFYLIAILFIIFDLEVVFILPFASVIHNVS-LLGGWITIIFLVILTIGFI
+nad3_apec N-SARVPFSFRFFLVAILFLLFDLEIALLFPLPFSVFFH--P--IHTP----LILTVGLI
+nad3_arath G-DARSRFDIRFYLVSILFLIPDLEVTFFFPWAVPPNKID-LFGFWSMMAFLFILTIGFL
+nad3_balca A-SARLPFSLRFFLVAILFLLFDLEIALLLPFPAALSARDPQLSFTLAFLILLILTIGLI
+nad3_chocr D-DARATFDIRFYLVAILFLIFDLEISFLFPWSLVLGEIS-IIGFWSMIVFLVILTIGFI
+nad3_drome S-SSRLPFSLRFFLITIIFLIFDVEIALILPMIIIMKYSNIMIWTITSIIFILILLIGLY
+nad3_human S-PARVPFSMKFFLVAITFLLFDLEIALLLPLPWALQTTNLPLMVMSSLLLIIILALSLA
+nad3_ktun S-SARLPFSMRFFLITVVFLVFDVEIVLLLPYLFSSGWSIDVFSLVGSMMILVILIIGVL
+nad3_lter S-TARIPFSTRFFLLAIIFIVFDIEIVLLMPLPTILHTSDVFTTVTTSVLFLMILLIGLI
+nad3_marpo D-DARSRFDIRFYLVSILFIIFDLEVTFLFPWAVSLNKIG-LFGFWSMMVFLFILTIGFV
+nad3_metse G-TPGRPFSIRFFLIGILFLIFDLEISFLFPWCVVCNQVF-PFGYWTMIVFLAVLTLGLV
+nad3_picca R-QSRTTYSIKFILIAILFLPFDLELTSILPYTLSMYNTN-IYGLFILLYFLLPLIIGFI
+nad3_podan LGQNRTQFGVKFFIFALVYLLLDLEILLTFPFAVSEYVNN-IYGLIILLGFITIITIGFV
+nad3_prowi D-DARGRFDIQFYLVAILFIIFDLEVAFLFPWALTLNKIG-YFGFWSMMLFLFILTVGFI
+nad3_recam D-DARGAFDVRFYLVAILFIIFDLEVAFLFPWAVALSDVT-IFGFWTMFIFLLILTVGFI
+ ############################ #######
+
+
+ 130 140 150
+ =========+=========+=========+===
+nad3_parde YEWKKGALEWA----------------------
+nad3_acaca YEWQKGALEWD----------------------
+nad3_allma YEFVSGAITDSF---------------------
+nad3_apec FEWVQGGLDWAE---------------------
+nad3_arath YEWKRGASDRE----------------------
+nad3_balca YEWMEGGLEWAE---------------------
+nad3_chocr YEWYKGALEWE----------------------
+nad3_drome HEWNQGMLNWSN---------------------
+nad3_human YEWLQKGLDWTE---------------------
+nad3_ktun HEWSEGSLEWFSSSN------------------
+nad3_lter HEWKEGSLDWSS---------------------
+nad3_marpo YEWKKGALDWE----------------------
+nad3_metse YEWLKGGLEWE----------------------
+nad3_picca IEINTKAIYMTKMFNRNVKSMTSYVKYNNKI--
+nad3_podan YELGKSALKIDSRQVITMTRFNYSSTIEYLGKI
+nad3_prowi YEWRKGALDWS----------------------
+nad3_recam YEWKKGALDWE----------------------
+ ########
+
+
+
+
+
+
+
+
Parameters used
+Minimum Number Of Sequences For A Conserved Position: 9
+Minimum Number Of Sequences For A Flanking Position: 14
+Maximum Number Of Contiguous Nonconserved Positions: 8
+Minimum Length Of A Block: 5
+Allowed Gap Positions: None
+Use Similarity Matrices: Yes
+
+
Flank positions of the 3 selected block(s)
+Flanks: [48 60] [64 91] [114 128]
+
+New number of positions in nad3.pir-gb1: 56 (36% of the original 153 positions)
+
+
+
+